Burrows-Wheeler Aligner (BWA) is an efficient program that aligns
relatively short nucleotide sequences against a long reference
sequence such as the human genome. It implements two algorithms,
bwa-short and BWA-SW. The former works for query sequences shorter
than 200bp and the latter for longer sequences up to around 100kbp.
Home: http://bio-bwa.sourceforge.net/
References: /usr/doc/bwa-0.7.15/References